Thanks Bruce. one more question: This is my command (5 subjects)
mris_make_template lh sphere.reg subj1 subj2 subj3 subj4 subj5 ./Temp5subj.tif where I select sphere.reg as sphere surface. I assume 1) that the generated template Temp5subj.tif is in the Freesurfer buckner40 spherical space and 2) the mean and variance of the measure included in the new template are also in the buckner40 spherical space. Is that correct? In addition, could you simply explain what's the difference between lh.curv and lh.sulc. Both files look similar and include negative and positive valude, except that lh.sulc seems to be smoothed. Thanks. Best, Liang 2012/9/14 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > yes, you can use mris_make_template to generate these results (it's what > we used to create the tif files in the first place) > > On Fri, 14 Sep 2012, liang wang wrote: > > Dear Bruce, >> Thanks for pointing me those information. That .tif file includes the >> mean and >> variance for the population sample that was used in Freesurfer. I would >> like to get >> similar measures for our own subjects. I think I could use the surface >> file (like >> surf/?h.sulc) in each subject folder to compute the mean and variance, >> right? Is >> this file already in spherical template space? Thanks again. >> >> Best, >> Liang >> >> 2012/9/14 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Hi Liang >> >> yes, that information is encoded in the .tif file that is the >> target of >> the registration. You can use mrisp_paint to copy a frame out of >> $FREESURFER_HOME/average/?h.**average.curvature.filled.** >> buckner40.tif >> >> the tif file is 3 sets of triplets in different frames. The first is >> the mean of the measure, the second is the variance and the third is >> the degrees of freedom. The 3 triplets are for the curvature of the >> inflated surface, the sulc and mean curvature of the white surface. >> >> cheers >> Bruce >> >> On Thu, 13 Sep 2012, liang wang wrote: >> >> Dear FS folkers, >> I am working on a functional probabilistic atlas. I find >> that some functional >> regions (particular along a big sulcus) show quite high >> probability value over a >> large sample, whereas the probability for some regions are >> quite lower. I think >> this disparity could be accounted for by the anatomical >> variation on each surface >> node that appears while surface-based >> registering individual surface to the average >> template that was provided by Freesurfer. For instance, the >> anatomical variation >> could be pretty small within a big sulcus (like central >> sulcus). >> >> I assume that Freesurfer output a file which characterizes >> this type of anatomical >> variation. Could someone point me which file it is and how >> to use it to create a >> group-level measure in order to clear display somewhere has >> large variation. >> Thanks. >> >> Best, >> Liang >> >> -- >> Liang Wang, PhD >> Neuroscience of Attention and Perception Laboratory >> Princeton Neuroscience Institute >> Princeton University >> Princeton, NJ, 08540 >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine >> at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> >> -- >> Liang Wang, PhD >> Neuroscience of Attention and Perception Laboratory >> Princeton Neuroscience Institute >> Princeton University >> Princeton, NJ, 08540 >> >> >> >> -- Liang Wang, PhD Neuroscience of Attention and Perception Laboratory Princeton Neuroscience Institute Princeton University Princeton, NJ, 08540
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